We've covered footer and boilerplate content a lot here but Google's John Mueller brought it up again when answering a question in a Google Hangout this morning on Google+. At the 15:30 mark into the video, John describes that having footer or boilerplate content and links should not lead to a penalty, nor is the content or links in that section penalized, it is more that those blocks are not seen as the primary content on the page by Google.
Here is what he said:
I think the main thing to kind of consider, is if you are linking site wide from one web site in the footer for the example, or if you have text site wide in the footer. Then that is probably not the same weight as if you had that on some many different pages that are completely separate. So it is not so much the issue that it is in the footer, it is just well, we see this across so many other pages on this web site, that we think it is probably not the most relevant thing on the whole web site.
So for example, if you have to put a legal disclaimer on your footer of your web site for legal reasons. That doesn’t mean the rest of the content on those pages will be devalued. But rather, we will try to figure out, oh this is disclaimer that is across the site, so that if someone is specifically looking for this disclaimer, fine, we will show one of the pages from the site, but otherwise we won’t treat it as primary content for that page.
So having links in your footer may not been seen as so important by Google because it is not primary content on the page. The links and content aren't necessarily penalized but they may not be given as much weight.
Obvious stuff for most of you but good to hear it from Google.
Here is the video embed:
Forum discussion at Google+.